Good prepping is the key to a good result as you know already - it's about 60% of the whole job.
Your ceiling water stains can not be concealed by water based paints only, and will need at least one coat of an alkyd pigmented primer - after you have stripped back any peeling crud.
With paint - as with anything - name brands are your best investment for fewer coats will cover a lot better. And don't be shy about applying the stuff. With paint, more is best, and only morons dilute beyond factory spec's.
DO use a sealer over any surface fillers, or you will regret it!. Topcoats are just that - topcoats, and will not evenly cover unless the whole surface beneath is uniform (except maybe after 3 or four coats - ie: more expensive paint cost and more work).
Just my 2cents from half the world away - hope something here is helpful.
Cheers,
Dennis S.